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miRTarBase 2025: updates to the collection of experimentally validated microRNA-target interactions

Shidong Cui1,2, Sicong Yu1,2, Hsi-Yuan Huang1,2

  • 1School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R. China.

Nucleic Acids Research
|November 23, 2024
PubMed

Insights

The miRTarBase database now contains over 3.8 million validated microRNA-target interactions, including roles in drug resistance and biomarker discovery. This expansion offers deeper insights into gene regulation and therapeutic strategies.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • MicroRNAs (miRNAs) are small non-coding RNAs regulating gene expression post-transcriptionally.
  • Experimentally validated miRNA-target interactions (MTIs) are crucial for understanding cellular processes and disease.
  • Existing databases require significant expansion to encompass the growing body of MTI research.

Purpose of the Study:

  • To update and expand the miRTarBase database with a comprehensive collection of experimentally validated MTIs.
  • To incorporate novel data on miRNA interactions with therapeutic agents and oxidized miRNA sequences.
  • To enhance the utility of miRTarBase for research in molecular oncology, drug development, and biomarker discovery.

Main Methods:

  • Curated collection and integration of experimentally validated MTIs from scientific literature.
  • Inclusion of data on miRNA interactions with drugs, drug resistance, and toxicity.
  • Application of advanced Natural Language Processing (NLP) models, including LLAMA3 with prompt engineering, for efficient MTI and miRNA-disease association identification.
  • Addition of information on oxidized miRNA sequences and their regulatory impact.

Main Results:

  • The updated miRTarBase now houses over 3,817,550 validated MTIs from 13,690 articles, a substantial increase from previous versions.
  • New entries detail miRNA roles in drug resistance, therapeutic strategies, and as biomarkers for toxicity and clinical treatment.
  • Expanded miRNA-mRNA and miRNA-miRNA networks facilitate the identification of key regulatory genes and co-regulatory miRNAs.
  • Integration of LLAMA3 model enables efficient MTI and miRNA-disease association discovery without extensive training data.

Conclusions:

  • The expanded miRTarBase serves as an indispensable resource for researchers in molecular oncology, drug development, and precision medicine.
  • The database provides critical insights into miRNA functions, regulatory networks, and their implications in therapeutic interventions and disease management.
  • Enhanced data integration and a redesigned user interface improve accessibility and facilitate deeper exploration of miRNA biology.

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